R help - Jan 2005 - Multiple comparisons following nlme

Dear Madam or Sir,

 

I need to do multiple comparisons following nlme analysis (Compare the
effects of different treatments on a response measured repeatedly over time;
fixed = response ~ treat*time). On the web I found the notion that one might
use the L argument from ANOVA. Do you have an example to show how this works
together with nlme?  Are there other ways to do a post-hoc analysis in nlme?

 

Thank you very much.

 

Stefan Uhlig

 

Prof. Dr.Stefan Uhlig

Head Division Pulmonary Pharmacology

Research Center Borstel

Leibniz Center for Medicine and Biosciences

23845 Borstel

Germany

Tel. 04537-188 478

FAX 04537- 188 778

suhlig@fz-borstel.de

 


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> I need to do multiple comparisons following nlme analysis (Compare
> the effects of different treatments on a response measured 
> repeatedly over time;
> fixed = response ~ treat*time).
If you have an interaction it does not really make sense to conduct a
multiple comparison because the difference in treatment depends on time,
i.e. this presumed post-hoc test could only give you a correct result for
one of your points in time. Why not conduct this analysis and then interpret
the pattern based on the estimates of your parameters and/or on a graphical
display of your data?

If your interaction is non-significant and you drop it, you still have a
mulitvariate problem and I have never come across a multiple comparison test
for such multivariate problems (but perhaps someone else has a pointer). In
your case it might be enough to carefully decide on how the set contrasts.

Then, an additional issue would be what kind of multiple comparisons to
conduct (for univarite anova's there are at least a dozen methods). You can
always conduct several to see which of the comparisons are highly
significant and which ones might not be so strong. But usually you do not
learn more than what you get when you interpret your parameters and/or
graphs of your data.

... and by the way, I guess your model is using lme (linear mixed effects
model) in package nlme and not actually an nlme (non-linear mixed effects
model) itself.

Regards, Lorenz
- 
Lorenz Gygax, Dr. sc. nat.
Centre for proper housing of ruminants and pigs
Swiss Federal Veterinary Office, agroscope FAT T?nikon

> I need to do multiple comparisons following nlme analysis (Compare
> the effects of different treatments on a response measured 
> repeatedly over time;
> fixed = response ~ treat*time).
I don't believe there exists a nice interface for doing this, but you can do
it "by hand". You need to obtain the point estimates of contrasts of
interest, and the estimated covariance matrix for those estimates. You can
then use these as arguments to csimint() in the multcomp package. 

--Jim

James A. Rogers 
Manager, Nonclinical Statistics
PGR&D Groton Labs
Eastern Point Road (MS 8260-1331)
Groton, CT 06340
office: (860) 686-0786
fax: (860) 715-5445
 


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